Transformed industrial bacillus strains and methods for making and using them

ABSTRACT

Novel methods and novel industrial unicellular microorganism strains, particularly industrial Bacillus strains, are provided for enhanced production of endogenous and exogenous polypeptides. Cloning vehicles containing the gene expressing the polypeptide of interest are introduced into a compatible host. Transformed hosts harboring the introduced vehicle in a stable way by integration of the vehicle into the host cells chromosome are selected. Efficient transfer of the vehicle containing the gene of interest is achieved, with the resulting industrial strain transformants being effective, stable producers of the desired polypeptide product.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 07/993,785, filed Dec. 21, 1992, now U.S. Pat. No. 5,624,829, which is a continuation of U.S. application Ser. No. 07/658,173, filed Feb. 19, 1991, now abandoned, which is a continuation of U.S. application Ser. No. 07/015,110, filed Feb. 17, 1987, now abandoned, which is a continuation-in-part of U.S. application Ser. No. 06/627,589, filed Jul. 3, 1984, now abandoned. All of which are incorporated herein by reference.

BACKGROUND OF THE INVENTION

1. Field of the Invention

There is substantial interest in employing industrial unicellular microorganism strains as hosts with recombinant DNA to produce polypeptides in high yields. Many industrially important enzymes, such as amylolytic and proteolytic enzymes, are produced by microorganisms of the genus Bacillus, e.g., B. subtilis, B. amyloliquefaciens, B. licheniformis, B. stearothermophilus and B. coagulans. In fermenters, strains are employed which are highly robust and stable. Furthermore, the strains are resistant to phage infection and, in addition, to genetic exchange, that is introduction of DNA by conventional transformation procedures. The conventional industrial strains are also prototrophic, in order to avoid adding expensive amino acids to the nutrient medium. Other characteristics of industrial strains are their high productivity until the end of the fermentation, which can be as long as a week, stable cell concentration upon exhaustion of the broth, and high productivity, usually at least 0.5% w/v of a specific secreted protein. In addition, it is often found with Bacilli, that there is a substantial secretion of DNAses, so that there is substantial degradation of any DNA in the medium.

Due to the genetic modification resistant nature of the industrial strains and their prototrophic character which makes them difficult to starve, they show resistance to transformation. It would therefore be of great value to provide for an efficient process for introducing DNA into industrial strains, where the DNA would be stably maintained in the industrial strain, there would be no loss or substantially no loss of viability and activity of the industrial strain and high yields of endogenous and exogenous polypeptide or protein products could be obtained.

Furthermore, selection of cells is difficult where the modification or transformation of the host cells involves increasing the copy number of an endogenous gene or previously introduced gene, where the gene is not involved with survival selection. Stability of extra copies of an endogenous gene or new genes is of utmost importance to ensure possible use of such genetically modified strains for industrial purposes.

It is therefore highly desirable to have an efficient process in which the stable presence of additional genes (increased copy number) can be detected for and stable chromosomal integration of these additional genes can be selected for.

2. Description of the Prior Art

Genetic manipulations of B. subtilis have been reported by Yoneda et al., Biochem. Biophys. Res. Commun. (1973) 50:765-770; Yoneda and Maruo, J. Bacteriol. (1975) 124:48-54; Sekiguchi et al., J. Bacteriol. (1975) 121:688-694; Hitotsuyanagi et al., Agri. Biol. Chem. (1979) 43:2342-2349; Yoneda, Appl. Env. Microbiol. (1980) 39:274-276.

Introduction of DNA into Bacillus without using conventional procedures for transformation of competent cells has been described. Protoplast transformation for several species of gram positive microorganisms is, for example, reported. Protoplast transformation of Bacillus subtilis has been described by Chang and Cohen. Molec. Gen. Genet. (1979) 168:111-115. Similar protocols were described: for the transformation of Bacillus megaterium protoplasts by Vorobjeva et al., FEMS Microbiol. Lett. (1980) 7:261-263 and by Brown and Carlton, J. Bacteriol. (1980) 142:508-512; the transformation of Bacillus amylolique-faciens protoplasts by Smith et al., Applied Environmental Microbiol. (1986) 51:634-639; for the transformation of Bacillus thuringiensis protoplasts by Fisher, Lithy and Schweitzer, Arch. Microbiol. (1984) 139:213-217 and by Miteva et al., FEMS Microbiol. Lett. (1981) 12:253-256; for Bacillus sphaericus by McDonald and Burke, J. Gen. Microbiol. (1984) 130:203-208; for Clostridium acetobutyliticum by Lin and Biascheck, Appl. Environ. Microbiol. (1984) 48:737-742; for Streptococcus lactis by Kondo and McKay, Appl. Environ. Microbiol. (1984) 48:252-259.

Fusion of bacterial protoplasts has been reviewed by Hopwood, Ann. Rev. Microbiol. (1981) 35:237-272, and this technique has been shown to be useful in the transfer of plasmids among different species by Dancer, J. Gen. Microbiol. (1980) 121:263-266.

Apart from polyethylene glycol induced protoplast fusion and protoplast transformation, other methods of introducing DNA into protoplasts can be developed such as fusion with DNA containing liposomes, as described by Holubova et al., Folia Microbiol. (1985) 30:97-100.

Successful applications of recombinant DNA technology with respect to production improvements of certain, efficiently transformable laboratory strains of B. subtilis have been reported, e.g., α-amylases, β-lactamases, dihydrofolate reductase, interferon and insulin (Palva, Gene (1982) 19:81-87; Shinomiya et al., Agric. Biol. Chem. (1981) 45:1733-1735; Gray and Chang, J. Bacteriol. (1981) 145:422-428; Williams et al., Gene (1981) 16:199-206; Palva, Gene (1983) 22:229-235). The difficulties in genetically manipulating Bacillus licheniormis soil isolates is reported by Thorne and Stull, J. Bacteriol. (1966) 91:1012-1014 and by Maruo and Tojo, J. Gen. Appl. Microbiol. (1985) 31:323-328. Segregational and structural instability of recombinant plasmids is considered as a major problem in using Bacillus, more specifically Bacillus subtilis as a host organism. These problems have been described by Ehrlich and Niaudet and by Kreft and Hughes in Current Top. Microbiol. Immunol. (1982) 96:19-29 and 1-17, respectively (ed. Holscheider and Goebel, Springer Verlag, N.Y.).

Chromosomal integration and chromosomal amplification of genes in prokaryotic genomes has been reported by Gutterson and Koshland, Proc. Natl. Acad. Sci. USA (1983) 80:4894-4898; Saito, Anzai and Kawamura, Genetics of Industrial Microorganisms, Proc. of the 11th Int. Symposium, ed. Ikeda and Beppu, Tokyo (1982) 125-130; Young, Gen. Microbiol. (1984) 130:1613-1621, Williams and Szalay, Gene (1983) 24:37-51 and in PCT patent application Ser. No. 84/00381. See also, U.K. Patent Application 2091628; European Patent Application 0 034 470.; European Patent Application 0 032 238; and European Patent Application 0 077 109, which disclosure is incorporated herein by reference, as it relates to pUR1523.

SUMMARY OF THE INVENTION

Novel methods and products involving genetically modified unicellular microorganism strains, particularly industrial Bacillus strains, are provided. Extrachromosomal DNA containing a gene Of interest capable of expression in an industrial strain host is introduced into an appropriate bacterial host, conveniently a laboratory strain host related to the industrial strain, and the modified bacterial host itself, or the extrachromosomal DNA containing the gene of interest isolated from this modified bacterial host, is combined with an industrial strain under fusing conditions.

Cells of the industrial strain containing the gene(s) of interest stably incorporated in their chromosome are selected by means of a marker associated with the gene of interest. To enable this chromosomal integration, a DNA sequence homologous to the chromosome DNA of the industrial strain is incorporated in the vector molecule. By the chromosomal integration stable maintenance and expression of the gene of interest by the industrial strain is obtained.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a diagrammatic view of the plasmid pGB33;

FIG. 2 is a diagrammatic view of the plasmid pGB34;

FIG. 3 is a diagrammatic view of the plasmid pLC28;

FIG. 4 is a diagrammatic view of the plasmid pLC83;

FIG. 5 i9 a diagrammatic view of the plasmid pLC87;

FIG. 6 is a diagrammatic view of the plasmid pGB35;

FIG. 7 is a diagrammatic view of the plasmid pLP33;

FIG. 8 is a diagrammatic view of the plasmid pLP87;

FIG. 9 is a SDS polyacrylamide gel-electrophoretogram of products secreted by various Bacillus industrial strains relative to protein molecular weight marker.

DESCRIPTION OF THE SPECIFIC EMBODIMENTS

Methods are provided for the genetic manipulation of industrial unicellular microorganism strains for use in fermentation for the production of polypeptide products in good yield. Bacillus strains will be used as paradigmatic of other microorganisms. The resulting modified industrial strains retain the desirable characteristics of industrial strains, while providing enhanced yields of expression product of endogenous (same genus or species) or exogenous (different genus) genes. That is exogenous intends genes which are not normally found in the genus to which the wild-type strain belongs.

The method involves introducing extrachromosomal DNA into a bacterial host, which is capable of replicating the DNA and is readily susceptible to the introduction of the extrachromosomal DNA. The modified bacterial host cell containing the extrachromosomal element or the isolated extrachromosomal element is then combined with the industrial Bacillus strain under fusing conditions, where the recipient Bacillus cells may be subsequently selected for the presence of the gene or genes of interest originating with the extrachromosomal element.

The subject invention may be divided up into the following parts: (1) preparation of the plasmid construct, including the gene(s) for which enhanced expression in the Bacillus host is desired and including DNA sequences which are homologous to that of the industrial host strain which is to be transformed; (2) cloning of the plasmid construct in a compatible host, which can be used for fusion with the industrial Bacillus strain or for isolating the plasmid construct from (3) introduction of the plasmid construct into protoplasts of the industrial Bacillus strain by protoplast fusion with protoplasts of the compatible host strain or protoplast transformation, including selection of derivatives of the industrial strain that contain the plasmid construct stably incorporated in their chromosome; and (4) growing of said strain in an appropriate nutrient medium for production of the expression product of the gene(s) of interest.

The gene(s) of interest may be any prokaryotic or eukaryotic gene. These genes may include bacterial genes, unicellular microorganism genes, e.g. bacterial genes, fungal genes, etc., mammalian genes or the like. The structural genes may be prepared in a variety of ways, including synthesis, isolation from genomic DNA, for example, by fragmentation using restriction enzymes or mechanical means, e.g. shearing, preparation from cDNA, or combinations thereof. The various techniques of manipulation of the genes are well-known, and include restriction digestion, resection, ligation, in vitro mutagenesis, primer repair, employing linkers and adapters, and the like. Thus, DNA sequences obtained from a host may be manipulated in a variety of ways, depending upon the requirements of the DNA construction. See Maniatis et al., Molecular Cloning, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1982.

Where the gene is obtained from a host which has transcriptional and translational initiation and termination regulatory signals which are recognized by (functional in) the industrial Bacillus strain, it will usually be convenient to maintain the 5'- and 3'-flanking regions of the structural gene to provide a cistron capable of expression in the industrial Bacillus host. The transcriptional initiation region may provide for constitutive or inducible expression, so that in appropriate situations, the host may be grown to high density before high levels of expression of the structural genes of interest are obtained. Alternatively, the native transcriptional initiation region may be substituted to enhance expression, provide for inducible expression, or the like.

Where the structural gene is from a source whose regulatory signals are not recognized by Bacillus, it will be necessary to obtain regulatory regions recognized by Bacillus and insert the structural genes between the initiation and termination regulatory signal. In some instances the exogenous structural gene with its own stop codon(s) may be inserted in reading frame behind the N-terminus codons of an endogenous Bacillus structural gene having its natural regulatory signals. The resulting product may then have some, for example, 0 to 30, additional N-terminal amino acids. Alternatively, operons can be prepared, where a single promotor provides for transcriptional initiation of a messenger RNA which code for a plurality of polypeptides.

In some instances, it may be desirable that the expression product be secreted. Where the expression product is naturally secreted and the leader signal and processing signal(s) are recognized by the Bacillus host, this will entail no difficulty. However, where the product is not normally secreted, or Bacillus does not recognize the secretory signals and/or processing signal(s), that is, the signals are not functional to a satisfactory degree in Bacillus, then it may be necessary to isolate or synthesize DNA sequences coding for secretory signals and processing signal(s) of a Bacillus polypeptide and join them to the 5'-end of the structural gene in proper reading frame.

The structural genes may express such a variety of polypeptides or protein such as enzymes hormones, lymphokines, surface proteins, blood proteins, structural proteins, immunoglobulins, or the like, from mammals, unicellular microorganisms, e.g., bacteria, fungi, such as yeast, or filamentols fungi, algae, protozoa, etc., plants, or other DNA source. Of particular interest are enzymes, more particularly hydrolases and more particularly proteases and saccharidases. Illustrative of such enzymes are endopeptidases, exopeptidases, serine and non-serine proteases, α- and β-amylases (particularly thermostable α-amylase), and the like.

There are a wide number of vectors which can be employed for the compatible host as well as the Bacillus strain, where the replication systems may be the same or different for the compatible host and the Bacillus strain. (By vector is intended a replication system(s) compatible with one or more hosts, usually a marker or selection in the host and at least one convenient, usually unique, restriction site.) Included among useful vectors are plasmids, cosmids and bacteriophages. Usually, it will be convenient to have as the compatible host, a non-industrial or laboratory Bacillus strain, although this is not necessary and in some instances other organisms may be used, such as E. coli. The vector will include one or more replication systems so that it is at least capable of being cloned in the compatible host. The replication system can provide for either high or low copy number, preferably a copy number of at least about 10 and generally not more than about 100.

Even when one desires integration of the structural genes in the industrial Bacillus strain and not maintenance on an extrachromosomal element, a replication system for Bacillus may be included. If a replication system is included, one provides for stretches of homology in the vector or plasmid construct with the Bacillus genome to enhance the probability of recombination and to be able to select for cases in which chromosomal integration took place. Either single or double cross-over recombination can be obtained, controlled in part by the nature of the flanking regions.

In addition to the replication system, there will usually be at least one marker and there may be more than one marker, usually not more than about three markers. By marker is intended a structural gene capable of expression in a host, which provides for survival selection. By "survival selection` is intended imparting prototrophy to an auxotrophic host, biocide or viral resistance. For prototrophy, various genes may be employed, such as leu, ura, trp, or the like. For biocide resistance this may include resistance to antibiotics, e.g. neo, cam, tet, tun, kan, or the like. Other markers include resistance to heavy metals, immunity, and the like.

Markers when used for chromosomal integration have to fulfill the demand that survival selection is possible even if only one or a few copies of the marker gene is present in the industrial host strain.

The various DNA sequences may be derived from diverse sources and Joined together to provide for a vector which includes one or more convenient, preferably unique, restriction sites to allow for insertion or substitution of the structural genes at such sites or in place of lost fragments to provide the plasmid construct.

Once the plasmid construct has been prepared, it may now be cloned in an appropriate auxiliary host referred to as the compatible or cloning host. Any host may be used which is convenient, is readily transformable, allows for replication of the plasmid construct without mutation of the foreign DNA and transfer to the industrial Bacillus strain in the presence of a fusogen, including fusion. Conveniently, polyethylene glycol of 1000 to 8000 is employed. A large number of laboratory strains are available which have a high efficiency of transformation and are usually auxotrophic and/or antibiotic sensitive. The use of a Bacillus host for cloning of the plasmid construct has the advantages that it permits the use of a single replication system as well as the same marker for survival selection in both the compatible host and the industrial strain. Thus, for the most part, the plasmid construct will be cloned in an appropriate Bacillus host. The Bacillus host need not be the same Bacillus strain as the industrial host and will be chosen primarily for convenience.

The plasmid construct may be introduced into the compatible host in accordance with conventional techniques, such as transformation, employing calcium precipitated DNA, conjugation, or other convenient technique. The compatible host may then be grown in an appropriate nutrient medium, under selective conditions to select for a host containing the plasmid construct. For auxotrophic hosts, the nutrient medium is deficient in the required nutrient, while for biocide resistance, a cytotoxic amount of the biocide(s), e.g. antibiotic(s), is employed in the nutrient medium. After growing the compatible host to a sufficient density, the compatible host is then treated to prepare the cells for fusion or the plasmid construct is isolated from the compatible host and used as such to transform the industrial host strain.

If fusion is to be used, conveniently, the cells are killed with a cytotoxic agent prior to or during protoplast formation.

Various cytotoxic agents may be employed, including antibiotics, but iodoacetamide is found to be convenient, efficient, and does not interfere with the subsequent fusion. Protoplasts are prepared from the cells in accordance with conventional ways, e.g., lysozyme or zymolase treatment, and the protoplasts carefully suspended in an appropriate medium having proper osmolarity for maintaining the integrity of the protoplast.

The industrial Bacillus acceptor strain is also treated to form protoplasts in a similar manner as the compatible host strain, but viable cells are employed for preparing protoplasts. Various Bacillus strains may be employed which have the desired traits of an industrial Bacillus strain, such as subtilis, licheniformis, amyloliquefaciens, stearothermophilus, and coagulans, preferably licheniformis and subtilis. The industrial Bacillus strains originate from organisms which may be isolated in the soil or available from depositories or other sources and are obtained by genetic modification of such Bacillus strains. The industrial Bacillus strains are characterized by being resistant to genetic exchange, such as phage infection or transformation. The strains are stable and may or may not be capable of spore formation. They are prototrophic and modified to provide for high yields of endogenous protein products, such as the enzymes α-amalyse and various proteases. The yield of such an endogenous protein product obtained in an industrial production process amounts to at least 5 g/L (0.5% w/v) for such an industrial strain. They also are found to secrete DNAses, which result in the degradation of DNA in the medium, providing for protection against genetic exchange.

The dead compatible host protoplast or the plasmid construct isolated from the compatible host and the viable industrial Bacillus host protoplast are combined in the presence of an appropriate fusogen. While any fusogen may be employed which provides a desired efficiency, for the most part polyethylene glycol is found to provide high efficiency of fusion with great convenience. If protoplast fusion is used, the ratio of the dead protoplast to the Bacillus acceptor strain will be preferably at least 1:1 and excesses of the dead protoplast may be employed. A short time after incubation of the dead protoplast, carrying the plasmid, construct, or of the isolated plasmid construct with the acceptor strain protoplasts, the fusogen mixture is replaced with an appropriate nutrient medium and cells regenerated in a selective medium, conveniently by plating on an agar plate.

After incubation of these plates, clones are screened that contain the plasmid construct as an integral part of their chromosome. This is done by isolation of total cellular DNA and selection for those clones in which no free plasmid DNA can be detected, whereas the marker gene of the plasmid is expressed.

The clones may then be screened in appropriate ways for detection of the expression of the additional structural genes. Various techniques may be employed, particularly where enzymes are involved which have well established methods of detection. Alternatively, where enzymes are not involved or there is no available detection system, antibodies, DNA or RNA hybridization, or bioassays can be employed for screening the clones to determine the presence of the plasmid construct and expression of the structural gene(s) of interest.

The industrial Bacillus host containing the plasmid construct or chromosomally integrated plasmid constructs or fragments thereof is then grown in a nutrient medium under conventional fermenting conditions. The fermenting may be continued until the broth is exhausted. Where the product has been secreted, the product may be isolated from the broth by conventional techniques, e.g., extraction, chromatography, electrophoresis, or the like. Where the product is retained in the cytoplasm, the cells may be harvested by centrifugation, filtration, etc., lysed by mechanical shearing, detergent, lysozyme, or other techniques and the product isolated as described previously. By employing the subject method greatly enhanced yields of endogenous polypeptides can be achieved, usually at least about 150% times the yield of the parent cell, more usually at least 75%, and preferably at least about 200% times the yield of the parent cell.

The following examples are offered by way of illustration and not by way of limitation.

EXPERIMENTAL Example I

Isolation of chromosomal DNA

Chromosomal DNA of B. licheniformis industrial strain T5, deposited with Central Bureau voor Schimmelcultures, Oosterstraat 1, Baarn, the Netherlands (hereinafter CBS) on Jul. 6, 1983 under No. 470.83, was isolated from 3L cultures, that were grown overnight at 37° C. under aeration. Cells were spun down at 10,000 rpm for 10 min. in a Sorvall CSA rotor, suspended in 10 ml sucrose-Tris buffer containing 25% w/v sucrose and 50 mM Tris-HCl pH 8.0, and lysed by addition of 0.5 ml lysozyme solution (20 mg/ml) and incubation for 15 min. at 37° C. After addition of 2 ml EDTA (0.5M) and incubation for 5 min. at 0° C., 1 ml 20% (w/v) sodium dodecyl sulphate (SDS) was added. The suspension was then extracted with a 1:1 phenolchloroform mixture. The supernatant was separated and carefully overlayed by 2 volumes of pure ethanol after which the DNA was isolated with the aid of a glass rod. After dissolving in distilled water containing 10 μg/ml ribonuclease, the DNA suspension was extracted with 1:1 phenol-chloroform, precipitated with 2 volumes of ethanol and resuspended in TE buffer (i.e., 10 mM TrisHCl, pH 8.0 containing 1 mM EDTA).

Example II

Isolation of plasmid DNA

B. subtilis strain lG 20, containing plasmid pUB110 (cf. European Patent Specification 0 021 468), was grown overnight in 1L penassay broth medium to which 5 μl/ml neomycin had been added. After centrifuging for 15 min. at 5000 rpm in a Sorvall model GSA rotor and resuspending in 15 ml sucrose-Tris buffer, the cells were lysed and treated with EDTA and SDS as described in Example I. After addition of NaCl to a final concentration of lM the supernatant was stored overnight at 4° C. and then centrifuged for 45 min. at 12500 rpm in a Sorvall type SS 34 rotor. The upper 70% (v/v) of the supernatant was treated with 20 μg/ml DNAse-free RNAse (for 0.5 h at 37° C.), and extracted with phenol-chloroform (1:1) mixture, followed by extraction by chloroform alone.

The DNA was precipitated from the extracted supernatant by addition of 0.2 volume of 5M NaCl and 0.25 volume of 40% (w/v) polyethylene glycol 6000, followed by incubation for 16 h at 4° C. After precipitation and centrifugation (30 min. at 12,500 rpm, Sorvall type SS 34 rotor) the DNA was resuspended in 2-3 ml TE buffer (as in Example I) and the dispersion made pH12.0 with 4M NaOH and maintained at this pH for 5 min. The pH was then adjusted to 8.5, and the suspension was extracted with phenol. After precipitation of the extract with ethanol the plasmid DNA was resuspended in a small volume of TE buffer.

Plasmid pUR1523 (cf. European specification A-77109) DNA from E. coli was isolated according to the method described by Birnboim and Doly, Nucl. Acids Res. (1979) 7:1513-1523.

Example III

a) Construction of the α-amylase containing recombinant plasmids pGB33 and pGB34 (FIGS. 1 and 2)

5 μg chromosomal DNA, isolated from the Bacillus production strain T5 (as described in Example I) and 1 g pUB110, isolated from B. subtilis 1G 20 (as described in Example II) were digested with EcoRI. After thermal denaturation of the restriction enzyme for 7.5 min. at 65° C., the DNA was precipitated with ethanol and resuspended in 20 μl of a ligase mixture containing 20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 10 mM dithiothreitol (DTT), 0.2 mg/ml bovine serum albumin, 0.5 mMATP and 1 unit of T4 ligase (BoehringerMannheim). The mixture was ligated overnight at 4° C. The ligated mixture was transferred into B. subtilis as described in Example IV below. Plasmid DNA was isolated (using the method described in Example II) from selected recombinant microorganisms and analysed with restriction endonucleases. Plasmid pGB33 was a recombinant of pUB110 and a chromosomal EcoRI fragment of approximately 3 kbp, containing the α-amylase cistron. Digesting pGB33 with the restriction endonucleases HindIII and BamHI, followed by S₁ exonuclease resection and ligation with T₄ yielded pGB34 (FIG. 2), which still harbors the α-amylase cistron but lacks a DNA segment containing many inconvenient restriction sites. The plasmids pGB33 in B. subtilis 1-85 (=trp⁻) and pGB34 in B. subtilis 1S-53 (Bacillus Genetic Stock Center, Ohio, U.S.A.) were deposited with CBS on Jul. 6, 1983 as Nos. 466.83 and 467.83, respectively.

b) Construction of the chymosin containing recombinant plasmids pLC28, pLC83 and pLC87 (FIGS. 3, 4 and 5).

0.5 g pGB34 DNA and 0.5 μg pUR1523, an E. coli plasmid that harbors the gene for bovine chymosin, were digested with PstI. After thermal denaturation and ligation as described in Example IIIa, the mixture was used for transformation. Plasmid DNA isolated from selected transformants (using the selection procedure described in Example IV below) was analysed with restriction endonucleases. The selected plasmid, called pLC28, was a recombinant of the chymosin gene containing PstI fragment of pUR1523, inserted into the unique PstI site of pGB34 (FIG. 3). Cutting pLC28 with the restriction endonuclease ClaI, followed by resection with the exonuclease Bal31 and ligation with T₄ ligase, yielded pLC83 (FIG. 4), which contains the gene for chymosin, but no longer contains a DNA segment with many inconvenient restriction sites. The plasmids pLC28 and pLC83, both in B. subtilis lS-53, were deposited with CBS on Jul. 6, 1983 as Nos. 469.83 and 468.83, respectively. In order to place the chymosin gene in phase behind the α-amylase transcriptional and translational initiation regulatory sequences, pLC83 was digested with PstI, resected with nuclease S₁ and ligated with T₄ ligase. The plasmid obtained was called pLC87, and shown to have the correct placement and orientation by sequence analysis. See FIG. 5.

c) Construction of the protease containing recombinant plasmids pLP33 and pnP87 (FIGS. 7 and 8).

100 μg chromosomal DNA of the protease producing strain B. subtilis 168 (Bacillus Genetic Stock Center, Columbus, Ohio) was partially digested with the restriction enzyme ClaI. After phenol extraction the DNA fragments were separated on a 1% agarose gel. By means of electroelution several DNA fractions were eluted from the gel and ligated with ClaI linearized pGB35 (a recombinant plasmid containing the Bacillus vector pGL112, W. M. de Vos, Thesis, University of Groningen 1983, and the α-amylase gene of pGB33, see FIG. 6). The ligation products were transferred into competent B. subtilis RUB331 cells in the manner as described in Example IV. The chloramphenicol-resistant transformants obtained were analysed for enhanced protease activity (prot⁺) and reduced α-amylase production capacity (amy⁻) (see Example IV) on 0.4% casein-amylose plates. Plasmid DNA was isolated from prot⁺ _(amy) ⁻ transformants and restriction site mapped; pLP33 appears to contain a 3.3 kbp ClaI fragment (FIG. 7) which includes a structural gene coding for a serine protease. pLP87 (FIG. 8) has a chromosomal ClaI insert of 1.8 kbp containing the genetic information for a non-serine protease.

Example IV

Transformation of Bacillus strains

B. subtilis 1-85 (trp⁻ amy⁻) transformed by incubating 1 ml cell suspension and 1 μg ligated DNA for 0.5 h at 37° C. with gentle shaking (Anagnostopoulos and Spizizen, J. Bacteriol. (1961)/81:741-746. Transformants were selected for antibiotic resistance on minimum medium agar plates, to which 0.02% (w/v) casamino acids (Difco) and 10 g/ml of an antibiotic were added. These transformants were then analysed for the presence of the desired structural gene.

In the case of α-amylase this was performed by looking for halos after covering the plates with a solution containing 0.6% (w/v) KI and 0.3% (w/v) I₂ ; by positive hybridization to a 32p labeled DNA probe synthesized in vitro in accordance with the N-terminal amino acid sequence of the biologically active enzyme; by immunoprecipitation with antibodies against the enzyme and by comparative isoelectrofocusing.

In the case of chymosin, positive selection was carried out via hybridization with 32p labeled pUR1523 DNA and by immunoprecipitation with antichymosin antibodies.

To identify the gene for a Bacillus protease the transformants were tested for their ability to form halos on casein minimal medium agar plates. The difference between serine and non-serine protease was determined by the method of Scheiner and Quigley (Anal. Biochemistry (1982) 122:58-69).

The selected transformants were used as donor strains in cell fusion experiments.

Example V

A. Cell fusion and regeneration

The transformed B. subtilis strain (B. subtilis strain 1-85 containing pGB33, B. subtilis strain lS-53 containing pLC87 or B. subtilis strain RUB331 containing pLP33) was grown overnight in 50 ml NBSG-X medium (Thorne and Stull, J. Bacteriol. (1966) 91:1012-1020 (Table II, page 1014) with a relevant antibiotic therein at 37° C. The cultures were diluted 1:1 with fresh NBSG-X medium and grown for another 1-1.5 h in the presence of 10 mM iodoacetamide. After centrifuging for 10 min. at 5000 rpm in a Sorvall type GSA rotor and resuspending in 10 ml SMM buffer containing 1.5M sucrose, 0.06M MgCl₂ and 0.06M maleate, protoplasts were formed by incubating the cells for 2 h at 37° C. in the presence of 2 mg/ml lysozyme. The protoplasts were spun down (10 min.×5000 rpm), resuspended in 5 ml SMML buffer (L-broth in which 1.5M sucrose, 0.06M MgCl₂ and 0.006M maleate has been dissolved), mixed and repelleted. After being resuspended, the protoplasts were mixed with the protoplasts of the acceptor strain T5, protoplasts prepared from viable cells as described above, and the resulting protoplasts incubated for 2 min. in the presence of approximately 30% (w/v) of polyethylene glycol 6000. After 1:3 dilution with SMML medium and centrifugation, the pellet was resuspended in a small volume of SMML medium. Then 100 μl aliquots were plated on regeneration agar plates containing 0.7% (w/v) K₂ HPO₄, 0.3% (w/v) KH₂ PO₄. 0.125% (w/v) (NH₄)₂ SO₄, 0.035% (w/v) MgSO₄.7H₂ O, 1.5% (w/v) agar, 3.7% (w/v) KCl, 0.1% (w/v) glucose, 0.01% (w/v) bovine serum albumin supplemented with 0.1% (w/v) spore solution containing 0.2% (w/v) MnSO₄, 0.2% (w/v) ZnSO₄, 0.2% (w/v) COCl₂, 0.5% (w/v) FeSo₄, 6% (w/v) NaCl and 0.5% (w/v) CaCl₂. Moreover these plates contained the relevant antibiotic, in the case of pGB33, and pLC87 100-160 μg/ml neomycin and in the case of pLP33 50 μg/ml of chloramphenicol.

After incubation at 37° C. for at least 72 h, the plates were replica plated on heart-infusion agar plates, containing also another antibiotic to which the acceptor strain is resistant but to which the donor strain is sensitive. Fusants designated as Type A were analysed according to the methods described in hereinafter. In the case of α-amylase the procedure was repeated as follows. Type A fusants were fused with B. subtilis protoplasts containing pGB36, a recombinant plasmid of pTL12, containing the gene that encodes resistance for trimethoprim (Tanaka and Kawano, Gene (1980) 10:131-136) and the EcoRI restriction fragment of pGB33, containing the gene that codes for B. licheniformis α-amylase, yielding fusants designated as Type B.

B. Protoplast transformation and regeneration

Protoplasts of the acceptor strain B. licheniformis T5, prepared as described above and resuspended in SMML buffer were incubated for 2 min. in the presence of approximately 30% polyethylene glycol 6000 with 1 μg of the plasmid pGB33, pLC87.or pLP33.

After this incubation these protoplast transformation experiments proceeded in an exactly identical way as described in Example V-A, by a dilution of 1:3 with SMML medium, centrifugation, resuspension of the cell pellet and plating of samples on regeneration agar plates containing the relevant antibiotics.

Example VI

Selection of fusants and transformants of Bacillus licheniformis T5.

Of the fusants and transformants prepared as described in the Example V-A and V-B, respectively, DNA was isolated according to the method of Holmes and Quigley (Anal. Biochem. (1981) 114:193-197). This DNA was analysed on agarose gels and it was found that depending on the plasmid used a certain percentage of the transformants did not contain free plasmid DNA, although the marker gene of the plasmid was expressed.

The following results were obtained:

    ______________________________________                                                       plasmid (free                                                                            percentage of                                          Acceptor      or in donor                                                                              fusants/transformants                                  strain        protoplasts)                                                                             without plasmid                                        ______________________________________                                         B. lich. T5   pGB33     10%                                                    B. lich. T5-Type A                                                                           pGB36     5%                                                     (pBG33)                                                                        B. lich. T5   pLP33     2%                                                     B. lich. T5   pLC87     <1%                                                    ______________________________________                                    

In the case of transformants or fusants in which the plasmid pGB33 was introduced, the plasmid containing B. licheniformis T5 strains were analysed in more detail. In all cases it was found that the plasmid underwent substantial deletions as the plasmids present had a molecular weight smaller than the molecular weight of pGB33. Upon transformation of these deleted plasmids back to the readily transformable strain Bacillus subtilis 1-85 (as described in Example IV) none of the neomycin resistant transformants showed amylase production.

Of the B. licheniformis T5 fusants or transformants in which pGB33 and pGB36 had been introduced and which were found to contain no free plasmid DNA, chromosomal DNA was isolated. This isolated DNA was characterized by genomic analysis using 32p labeled plasmid pGB33 and it was found that these fusants/transformants contained more than one intact copy of the Bacillus licheniformis amylase gene.

Example VII

Construction of a Bacillus industrial strain suited for efficient chromosomal integration of heterologous genes.

The plasmid pBC16 is derived from Bacillus cereus and is highly homologous to pUB110 as described by Polak and Novick, Plasmid (1982) 7:152-162.

The main difference between pBC16 and pUB110 is that pBC16 contains a tetracycline resistance gene where pUB110 has a neomycin resistance gene.

B. licheniformis T5, type A cells, harboring two amylase genes and one copy of pUB110 in their chromosome, were transformed using pBC16 linearized with XbaI, according to the protoplast transformation protocol as described in Example V. 10 μg/ml tetracycline was included in the regeneration plates. Selection for tetracycline resistant colonies resulted in a strain where the chromosomally located neomycin gene derived from pUB110 was replaced by the tetracycline gene of pBC16 by double reciprocal recombination.

The resulting strain T5-16 can be used as a suitable strain for efficient chromosomal insertion of pUBH110-derived plasmid constructs. Strain T5-16 is tetracycline resistant and neomycin sensitive, and has approximately 3 kb of DNA sequences homologous to pUB110 in its genome.

Example VIII

Integration of the chymosin gene contained in pLC87 into the chromosome of B. licheniformis T5-16.

B. licheniformis T5-16 was transformed with the plasmid pLC87 as described in Example V-B using the protoplast transformation protocol. After 2 days of incubation at 37° C. on minimal regeneration plates containing 10 μg/ml neomycin the transformants were streaked on minimal plates containing 10 μg/ml neomycin. By characterization of the DNA of these transformants as described in Example VI it was found that at least 95% of these transformants contained no plasmid DNA. By increasing the length of the homologous sequences between plasmid construct introduced and acceptor industrial strain the frequency of integration is considerably increased. Apparently only few, if any, of the transformants contain pLC87 both integrated in their chromosome and as free plasmid.

Isolation of chromosomal DNA, according to the protocol of Example 1, followed by digestion with suitable restriction enzymes and hybridization with 32p labeled pUR1523 showed that pLC87 carrying the chymosin gene had integrated at the expected position in the chromosome by homologous recombination of pUB110 sequences.

Example IX

Stability of chromosomally integrated chymosin genes versus genes present on extrachromosomal DNA.

The chymosin gene integrated in the chromosome of B. licheniformis strain T5-16 was maintained stably for 6 days during a fermentation. This was monitored by measuring the percentage of neomycin resistant cells throughout the fermentation. This percentage remained higher than 90%. When checked, neomycin resistant cells did not have a chromosomal deletion in the chymosin gene.

In fermentations where pLC87 was present as a free plasmid in strain T5, in general, instability was detected. After 2 days of fermentation more than 50% of the cells did not contain any intact plasmid, but only plasmids having deletions. The detected plasmids did not contain the complete chymosin gene. After more than 3 days, additional segregational instability of the plasmids was detected. After 6 days of fermentation less than 20% of the cells contained plasmid. Loss of plasmid correlated with loss of neomycin resistance.

Example X

Fermentative production of α-amylase, protease and chymosin by genetically engineered Bacillus production strains.

The genetically engineered production strain of B. licheniformis T5, obtained by fusion with the B. subtilis strain 1-85, containing pGB33 (as described in Example V), was cultivated for 7 days in an industrial nutrient broth under such fermentation conditions that the production of secreted α-amylase is at least 0.5% w/v. The production of this engineered strain was compared to the production of the parental strain B. licheniformis T5. As evidenced by an SDS polyacrylamide gelelectrophoretogram of products secreted by the production strain B. licheniformis T5 (see FIG. 9, lane 3) and those secreted by the genetically engineered strain B. licheniformis T5, containing pGB33 (see FIG. 9, lane 2), the production of α-amylase was significantly increased by the introduction of the plasmid pGB33.

Comparable results were obtained with the plasmid pLP33, which introduction improved the production of protease and with plasmid pLC87 which introduction resulted in a B. licheniformis T5 strain, which is capable of producing chymosin. Table I shows the summarized results of a quantitation of the improvements of the respective genetically engineered microorganisms.

                  TABLE I                                                          ______________________________________                                                               Chromosomal                                                                               α-amylase                               Organism   Plasmid    Integration                                                                               production                                    ______________________________________                                         B. licheniformis T5                                                                       --                    100%*                                         B. licheniformis T5                                                                       pGB33      -           50-100%                                      B. licheniformis T5                                                                       pGB33      +          180%**                                        B. lich.-T5 type A                                                                        pGB36      +          230%***                                       plasmid (pGB33)                                                                ______________________________________                                                                          protease                                                                       production                                    ______________________________________                                         B. licheniformis T5                                                                       --                    100%                                          B. licheniformis T5                                                                       pLP33      +          145%                                          ______________________________________                                                                          chymosin                                                                       production                                    ______________________________________                                         B. licheniformis T5                                                                       --                    -                                             B. licheniformis T5                                                                       pLC87      -          +                                             B. lich. T5-16                                                                            pLC87      +          +                                             ______________________________________                                          *1 amylase gene;                                                               **2 amylase genes;                                                             ***3 amylase genes.                                                      

The subject method has shown itself as highly successful with Bacillus. However, many unicellular microorganisms other than Bacillus find use in industrial fermentation and have properties such as the industrial Bacillus strains which make them refractory to efficient transformation. Therefore, the subject method could find application with industrial strains of other prokaryotic and eukaryotic organisms, such as other bacteria, fungi, e.g., yeast and filamentous fungi, protozoa, algae, etc. Species of genera, such as Aspergillus, Candida, Escherichia, Kluyveromyces, Penicillium, Pseudomonas, Saccharomyces and Streptomyces, are of particular interest.

Of particular interest in these organisms and in part as indicated for Bacillus is the industrial production of endogenous polypeptides, such as α-amylases, amylo-glucosidases, catalases, cellulases, chymosins, β-galactosidases, glucose isomerases, hemicellulases, invertases, lactases, lipases, pectinases, pectin esterases, penicillin-amidases, penicillinases, proteases, exo- and endopeptidases, pullulanases and xylanases. Also of interest are exogenous proteins, such as mammalian blood proteins, e.g., Factor VIII, both C and R, serum albumin, tissue plasminogen activator, other blood Factors, e.g., V, VI, VII, IX, X, XI and XII, lymphokines, interferons, e.g., alpha-, beta- and gamma-, mammalian enzymes, cell surface receptors, immunoglobulins, etc.

It is evident from the above results that a simple and efficient procedure is provided for stably introducing homologous or heterologous genes into the chromosome of industrial Bacillus strains, while retaining the desirable characteristics of the strains and providing for the enhanced competence of the cells in the increased production of a desired expression product endogenous to the Bacillus host or the production of a novel expression product of interest. High efficiencies of transfer are achieved and when substantial homology exists or is created between the plasmid construct and the industrial Bacillus strain chromosome, single or multiple copy integration of the structural genes is achieved. The integration of plasmid constructs was shown to result in a more stable situation for production fermentations as when extrachromosomal plasmid constructs were present. In the latter case extensive instability was detected.

The subject method greatly enhances the capability of modifying presently existing industrial Bacillus strains to provide efficient fermentative production of a wide variety of polypeptides and proteins of interest.

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims. 

What is claimed is:
 1. A method for producing an industrial Bacillus transformed strain comprising non-native DNA integrated into the chromosome of said transformed strain which non-native DNA encodes and effects production in said transformed strain of a polypeptide of interest and a marker polypeptide, said method comprising:combining the cells from which said transformed strain is derived as protoplasts with said DNA under fusing conditions, whereby said DNA is introduced into said protoplasts and integrated into the chromosome of said protoplasts to produce transformed protoplasts; and culturing said transformed protoplasts to produce cells of said transformed strain.
 2. The method according to claim 1 which farther comprises selecting for cells of said transformed strain by means of said marker polypeptide.
 3. The method according to claim 1, wherein said cells from which said transformed strain is derived are resistant to phage infection and introduction of DNA by conventional transformation procedures.
 4. The method according to claim 1, wherein said cells from which said transformed strain is derived do not stably maintain plasmid DNA under industrial fermentation conditions.
 5. The method according to claim 1, wherein said cells from which said transformed strain is derived are prototrophic.
 6. A transgenic industrial Bacillus strain comprising:a transgene coding for a polypeptide of interest whereby upon expression of said transgene, said transgenic industrial Bacillus strain produces at least about 150% of the amount of said polypeptide produced by a nontransgenic cell of the strain from which said transgene is obtained.
 7. The transgenic industrial Bacillus strain according to claim 6, wherein said Bacillus is Bacillus licheniformis.
 8. The transgenic industrial Bacillus strain according to claim 6, wherein said strain is obtained by inserting a vector selected from the group consisting of pLC87, pGB33, pGB36, and pLP33 into a nontransgenic cell of the strain from which said transgenic industrial Bacillus strain is derived.
 9. The transgenic Bacillus strain according to claim 6, wherein said polypeptide is an amylase.
 10. The transgenic industrial Bacillus strain according to claim 6, wherein said polypeptide is a protease.
 11. The transgenic industrial Bacillus strain according to claim 6, wherein said transgene comprises DNA endogenous to said Bacillus strain.
 12. The transgenic Bacillus strain according to claim 9, wherein said amylase is an α-amylase.
 13. The transgenic industrial Bacillus strain according to claim 9, wherein said transgenic industrial Bacillus strain contains two or more transgenes.
 14. The transgenic industrial Bacillus strain according to claim 10, wherein said protease is a serine protease.
 15. The transgenic industrial Bacillus strain according to claim 11, wherein said transgenic industrial Bacillus strain contains more than one copy of said transgene.
 16. A method for obtaining a polypeptide of interest, said method comprising:isolating said polypeptide of interest from a culture broth or a lysate of a transgenic industrial Bacillus strain which comprises and expresses a transgene coding for said polypeptide of interest and which produces at least about 150% of the amount of said polypeptide of interest produced by a nontransgenic cell of the strain from which said transgene is obtained.
 17. The method according to claim 16, wherein said polypeptide of interest is an amylase or a protease.
 18. The method according to claim 16, wherein said polypeptide of interest is an enzyme.
 19. The method according to claim 17, wherein said amylase is a thermostable amylase.
 20. The method according to claim 17, wherein said amylase is an α-amylase.
 21. The method according to claim 18, wherein said enzyme is chymosin or a precursor form of chymosin.
 22. A method for transforming cells of an industrial Bacillus strain to produce an industrial Bacillus transformed strain comprising non-native DNA integrated into the chromosome of said transformed strain which encodes and effects production of a polypeptide of interest and a marker polypeptide, said method comprising:(a) forming protoplasts of said cells; (b) combining said protoplasts With a DNA construct comprising said non-native DNA under fusing conditions such that said non-native DNA is introduced into said protoplasts and integrates into the chromosome of said protoplasts to produce transformed protoplasts, with the proviso that said DNA or the flanking sequences in said DNA construct command recombination with said chromosome of said protoplasts; and (c) culturing said transformed protoplasts to produce cells of said transformed strain.
 23. The method according to claim 22 which further comprises selecting for cells of said transformed strain by means of said marker polypeptide.
 24. The method according to claim 22 wherein said industrial Bacillus strain cells are resistant to phage infection and introduction of DNA by conventional transformation procedures.
 25. The method according to claim 22, wherein said industrial Bacillus strain cells do not stably maintain plasmid DNA under industrial fermentation conditions.
 26. The method according to claim 22, wherein said industrial Bacillus strain cells are capable of producing about 0.5% w/v of secreted protein under industrial fermentation conditions.
 27. A method for transforming cells of an industrial Bacillus strain to produce an industrial Bacillus transformed strain comprising non-native DNA integrated into the chromosome of said transformed strain which encodes and effects production of a polypeptide of interest and a marker polypeptide, said method comprising:(a) obtaining readily transformable Bacillus strain donor cells which are compatible with said industrial Bacillus strain cells and have been transformed with a DNA construct comprising said non-native DNA, with the proviso that said non-native DNA or the flanking sequences in said DNA construct command recombination with said chromosome of said transformed strain; (b) forming protoplasts of said Bacillus strain donor cells and said industrial Bacillus strain cells; (c) combining said Bacillus strain donor cell protoplasts with said industrial Bacillus strain protoplasts in the presence of a fusogen such that said non-native DNA integrates into the chromosome of said industrial Bacillus strain protoplasts to produce transformed protoplasts; and (d) culturing said transformed protoplasts to produce cells of said transformed strain.
 28. The method according to claim 27 which further comprises selecting for cells of said transformed strain by means of said marker polypeptide.
 29. The method according to claim 27, wherein said industrial Bacillus strain cells are resistant to phage infection and introduction of DNA by conventional transformation procedures.
 30. The method according to claim 27, wherein said industrial Bacillus strain cells do not stably maintain plasmid DNA under industrial fermentation conditions.
 31. The method according to claim 27, wherein said industrial Bacillus strain cells are capable of producing about 0.5% w/v of secreted protein under industrial fermentation conditions. 